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I am trying to compile hdf-4.2.11 for rhel 6; i have compiled required dependencies for hdf like zlib jpeg and szip using icc & ifort;
The configure script of HDF4 ran successfully ,
CC=$CCOMP F77=$FCOMP CXX=$CXXCOMP ./configure --prefix=$ROOT_DIR/hdf4 --with-zlib=$ROOT_DIR/zlib --with-jpeg=$ROOT_DIR/jpeg --with-szlib=$ROOT_DIR/szip
The configure log is :
CC=$CCOMP F77=$FCOMP CXX=$CXXCOMP ./configure --prefix=$ROOT_DIR/hdf4 --with-zlib=$ROOT_DIR/zlib --with-jpeg=$ROOT_DIR/jpeg --with-szlib=$ROOT_DIR/szip
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/home/puneet/hdf-4.2.11/bin/missing: Unknown `--is-lightweight' option
Try `/home/puneet/hdf-4.2.11/bin/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking shell variables initial values... done
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking if basename works... yes
checking if xargs works... yes
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.0.090 Build 20140723
Copyright (C) 1985-2014 Intel Corporation. All rights reserved.
checking whether make sets $(MAKE)... (cached) yes
checking for gcc... icc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether icc accepts -g... yes
checking for icc option to accept ISO C89... none needed
checking whether icc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of icc... gcc3
checking how to run the C preprocessor... icc -E
checking whether we are using the GNU C++ compiler... yes
checking whether icpc accepts -g... yes
checking dependency style of icpc... gcc3
checking whether we are using the GNU Fortran 77 compiler... no
checking whether ifort accepts -g... yes
checking how to get verbose linking output from ifort... -v
checking for Fortran 77 libraries of ifort... -L/opt/intel/composer_xe_2015.0.090/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/ -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/opt/intel/composer_xe_2015.0.090/compiler/lib/intel64/ -L/opt/intel/composer_xe_2015.0.090/mkl/lib/intel64/ -L/opt/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64/ -L/opt/intel/composer_xe_2015.0.090/ipp/lib/intel64/ -L/opt/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4/ -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether ln -s works... yes
checking for ar... ar
checking for bison... bison -y
checking for flex... flex
checking for diff... diff -w
checking for makeinfo... makeinfo
checking for neqn... neqn
checking for tbl... tbl
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by icc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from icc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if icc supports -fno-rtti -fno-exceptions... yes
checking for icc option to produce PIC... -fPIC -DPIC
checking if icc PIC flag -fPIC -DPIC works... yes
checking if icc static flag -static works... no
checking if icc supports -c -o file.o... yes
checking if icc supports -c -o file.o... (cached) yes
checking whether the icc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... icpc -E
checking for ld used by icpc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the icpc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for icpc option to produce PIC... -fPIC -DPIC
checking if icpc PIC flag -fPIC -DPIC works... yes
checking if icpc static flag -static works... no
checking if icpc supports -c -o file.o... yes
checking if icpc supports -c -o file.o... (cached) yes
checking whether the icpc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ifort option to produce PIC... -fPIC
checking if ifort PIC flag -fPIC works... yes
checking if ifort static flag -static works... no
checking if ifort supports -c -o file.o... yes
checking if ifort supports -c -o file.o... (cached) yes
checking whether the ifort linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: creating ./config.lt
config.lt: creating libtool
checking if we should install only statically linked executables... no
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for compress2 in -lz... yes
checking for compress2... yes
checking jpeglib.h usability... yes
checking jpeglib.h presence... yes
checking for jpeglib.h... yes
checking for jpeg_start_decompress in -ljpeg... yes
checking szlib.h usability... yes
checking szlib.h presence... yes
checking for szlib.h... yes
checking for SZ_BufftoBuffCompress in -lsz... yes
checking for szlib encoder... no
checking for xdr library support... yes
checking for ANSI C header files... (cached) yes
checking whether icc and cc understand -c and -o together... yes
checking how to run the C++ preprocessor... icpc -E
checking whether ifort understands -c and -o together... yes
checking size of int*... 0
checking whether byte ordering is bigendian... no
checking for build mode... production
checking for math library support... yes
checking for fork... yes
checking for system... yes
checking for vfork... yes
checking for wait... yes
checking if deprecated public symbols are available... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating libhdf4.settings
config.status: creating hdf/Makefile
config.status: creating hdf/examples/Makefile
config.status: creating hdf/fortran/Makefile
config.status: creating hdf/fortran/examples/Makefile
config.status: creating hdf/src/Makefile
config.status: creating hdf/test/Makefile
config.status: creating hdf/util/Makefile
config.status: creating hdf/util/h4cc
config.status: creating hdf/util/h4fc
config.status: creating hdf/util/h4redeploy
config.status: creating hdf/util/testutil.sh
config.status: creating man/Makefile
config.status: creating mfhdf/fortran/ftest.f
config.status: creating mfhdf/fortran/jackets.c
config.status: creating mfhdf/fortran/netcdf.inc
config.status: creating mfhdf/libsrc/netcdf.h
config.status: creating mfhdf/Makefile
config.status: creating mfhdf/dumper/Makefile
config.status: creating mfhdf/dumper/testhdp.sh
config.status: creating mfhdf/examples/Makefile
config.status: creating mfhdf/examples/testexamples.sh
config.status: creating mfhdf/fortran/Makefile
config.status: creating mfhdf/fortran/examples/Makefile
config.status: creating mfhdf/fortran/testfortran.sh
config.status: creating mfhdf/hdfimport/Makefile
config.status: creating mfhdf/hdfimport/testutil.sh
config.status: creating mfhdf/hdiff/Makefile
config.status: creating mfhdf/hdiff/testhdiff.sh
config.status: creating mfhdf/hrepack/Makefile
config.status: creating mfhdf/hrepack/hrepack.sh
config.status: creating mfhdf/hrepack/hrepack_all.sh
config.status: creating mfhdf/libsrc/Makefile
config.status: creating mfhdf/ncdump/Makefile
config.status: creating mfhdf/ncdump/testncdump.sh
config.status: creating mfhdf/ncgen/Makefile
config.status: creating mfhdf/ncgen/testncgen.sh
config.status: creating mfhdf/nctest/Makefile
config.status: creating mfhdf/test/Makefile
config.status: creating mfhdf/test/testmfhdf.sh
config.status: creating mfhdf/xdr/Makefile
config.status: creating hdf/src/h4config.h
config.status: executing h4config commands
modifying hdf/src/h4config.h
Post process libhdf4.settings
config.status: executing depfiles commands
config.status: executing libtool commands
SUMMARY OF THE HDF4 CONFIGURATION
=================================
General Information:
-------------------
HDF4 Version: 4.2.11
Configured on: Fri Apr 17 13:28:56 IST 2015
Configured by: puneet@shavakcuda
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux shavakcuda 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Libraries:
Installation point: /home/puneet/hdf4
Compiling Options:
------------------
Compilation Mode: production
C compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/icc ( Intel(R) C Intel(R) 64 Compiler Version 15.0.0.090 Build 20140723)
CFLAGS: -O
CPPFLAGS: -I/home/puneet/zlib/include -I/home/puneet/jpeg/include -I/home/puneet/szip/include -DSWAP
Shared Libraries: no
Static Libraries: yes
Statically Linked Executables: no
LDFLAGS: -L/home/puneet/zlib/lib -L/home/puneet/jpeg/lib -L/home/puneet/szip/lib
Extra libraries: -lsz -ljpeg -lz
Archiver: ar
Ranlib: ranlib
Languages:
----------
Fortran: yes
Fortran Compiler: /opt/intel/composer_xe_2015.0.090/bin/intel64/ifort ( Intel(R) Fortran Intel(R) 64 Compiler Version 15.0.0.090 Build 20140723)
FFLAGS:
Features:
---------
SZIP compression: enabled with decoder only
Support for netCDF API 2.3.2: yes
but while make ing ; i am getting following error:
libtool: compile: icc -DHAVE_CONFIG_H -I. -I/home/puneet/zlib/include -I/home/puneet/jpeg/include -I/home/puneet/szip/include -DSWAP -O -MT dfcomp.lo -MD -MP -MF .deps/dfcomp.Tpo -c dfcomp.c -o dfcomp.o mv -f .deps/dfcomp.Tpo .deps/dfcomp.Plo /bin/sh ../../libtool --tag=CC --mode=compile icc -DHAVE_CONFIG_H -I. -I/home/puneet/zlib/include -I/home/puneet/jpeg/include -I/home/puneet/szip/include -DSWAP -O -MT dfconv.lo -MD -MP -MF .deps/dfconv.Tpo -c -o dfconv.lo dfconv.c libtool: compile: icc -DHAVE_CONFIG_H -I. -I/home/puneet/zlib/include -I/home/puneet/jpeg/include -I/home/puneet/szip/include -DSWAP -O -MT dfconv.lo -MD -MP -MF .deps/dfconv.Tpo -c dfconv.c -o dfconv.o ": internal error: ** segmentation violation signal raised ** Access violation or stack overflow. Please contact Support. compilation aborted for dfconv.c (code 4) make[3]: *** [dfconv.lo] Error 1 make[3]: Leaving directory `/home/puneet/hdf-4.2.11/hdf/src' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/puneet/hdf-4.2.11/hdf/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/puneet/hdf-4.2.11/hdf' make: *** [all-recursive] Error 1
earlier i had compiled hdf4 using gnu compilers successfully; so i guess intel compilers are at fault here;
eagerly awaiting you replies!
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4 Replies
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If that bug persists in a current icc update, it definitely should be reported. Preferable reporting would be on premier.intel.com, if your support account is working, or possibly by attaching the reproducer here.
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i am using centos 6.5 as my development machine,
CXX_COMP=icc and F_COMP=ifort.
configure command:
LD_LIBRARY_PATH=$user1_install_path/Application_Dependencies/lib:$LD_LIBRARY_PATH CC=$C_COMP CFLAGS="-fPIC" LDFLAGS="-L$user1_install_path/Application_Dependencies/lib -lsz -lz -ljpeg" CPPFLAGS="-I$user1_install_path/Application_Dependencies/include" CXX="$CXX_COMP" CXXFLAGS="-fPIC" F77="$F_COMP" FFLAGS="-fPIC" ./configure --prefix=$user1_install_path/Application_Dependencies --with-zlib=$user1_install_path/Application_Dependencies/ --with-szlib=$user1_install_path/Application_Dependencies --with-jpeg=$user1_install_path/Application_Dependencies/ --enable-fortran --enable-netcdf
make
make install
Makefile is attached!
using this this error should be reproduced!
I don't have support account at present!
I am expecting a quick redressal of this problem , i even am ready to manually compile the dfconv.c file , please tell me the compiler flags !
i even tried:
icc -c dfconv.c
": internal error: ** segmentation violation signal raised **
Access violation or stack overflow. Please contact Support.
i have attached the dfconv.c !
-----------------------------------------------------------------UPDATE--------------------------------------------------------------------------
Thankyou , The same issue is posted here. v2015 update 3 fixed the compilation issue!
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Hi Puneet,
Can you please attach a preprocessed file to this thread so we can investigate this further?
Thanks,
Kittur
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Hi Puneet,
Please use the compiler option -E to generate the preprocessed version of the file.
Thanks and Regards
Anoop
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